Multiple sequence alignment - TraesCS3B01G377600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G377600 chr3B 100.000 4064 0 0 1 4064 594746416 594742353 0.000000e+00 7505.0
1 TraesCS3B01G377600 chr3B 94.703 1416 43 11 1248 2651 680235317 680233922 0.000000e+00 2170.0
2 TraesCS3B01G377600 chr3B 94.606 1409 46 10 1248 2646 733621798 733623186 0.000000e+00 2154.0
3 TraesCS3B01G377600 chr3A 91.193 3168 158 51 97 3187 595062515 595059392 0.000000e+00 4193.0
4 TraesCS3B01G377600 chr3A 83.788 623 88 6 3440 4049 574232407 574233029 2.720000e-161 579.0
5 TraesCS3B01G377600 chr3A 95.312 64 3 0 3312 3375 595059286 595059223 7.190000e-18 102.0
6 TraesCS3B01G377600 chr3D 93.223 2848 105 37 633 3410 452619953 452617124 0.000000e+00 4109.0
7 TraesCS3B01G377600 chr3D 87.403 516 33 9 97 584 452620953 452620442 7.630000e-157 564.0
8 TraesCS3B01G377600 chr5B 94.633 1416 44 11 1248 2651 411026787 411025392 0.000000e+00 2165.0
9 TraesCS3B01G377600 chr5B 87.574 169 21 0 3423 3591 2039169 2039001 3.200000e-46 196.0
10 TraesCS3B01G377600 chr1B 94.492 1416 46 11 1248 2651 353273958 353272563 0.000000e+00 2154.0
11 TraesCS3B01G377600 chr1B 81.439 1918 325 25 1086 2989 532693355 532695255 0.000000e+00 1541.0
12 TraesCS3B01G377600 chr7A 94.535 1409 47 11 1248 2646 608482219 608483607 0.000000e+00 2148.0
13 TraesCS3B01G377600 chr7A 84.404 654 89 6 3424 4064 85361905 85361252 7.410000e-177 630.0
14 TraesCS3B01G377600 chr7A 74.889 450 92 13 3421 3852 497617261 497616815 6.940000e-43 185.0
15 TraesCS3B01G377600 chr6B 94.464 1409 48 9 1248 2646 424069782 424071170 0.000000e+00 2143.0
16 TraesCS3B01G377600 chr1D 81.847 1917 319 23 1086 2989 397285115 397287015 0.000000e+00 1585.0
17 TraesCS3B01G377600 chr4B 93.324 734 25 8 1928 2651 396524267 396523548 0.000000e+00 1062.0
18 TraesCS3B01G377600 chr4B 80.851 94 12 5 2 92 276096321 276096231 7.290000e-08 69.4
19 TraesCS3B01G377600 chrUn 94.830 677 21 5 1970 2646 363668711 363669373 0.000000e+00 1044.0
20 TraesCS3B01G377600 chr7B 94.562 662 23 1 3414 4062 423764182 423763521 0.000000e+00 1011.0
21 TraesCS3B01G377600 chr7D 95.227 440 21 0 2328 2767 236582801 236582362 0.000000e+00 697.0
22 TraesCS3B01G377600 chr7D 86.310 168 21 1 3424 3591 529771627 529771462 8.970000e-42 182.0
23 TraesCS3B01G377600 chr6D 80.532 601 90 17 3420 4002 3289325 3288734 1.730000e-118 436.0
24 TraesCS3B01G377600 chr2D 80.303 594 103 6 3421 4001 55139540 55138948 1.730000e-118 436.0
25 TraesCS3B01G377600 chr4A 90.435 345 9 3 3419 3741 688563336 688562994 6.240000e-118 435.0
26 TraesCS3B01G377600 chr4D 79.899 597 97 13 3422 4002 253780345 253780934 2.260000e-112 416.0
27 TraesCS3B01G377600 chr6A 75.839 447 85 15 3423 3852 532542292 532541852 5.320000e-49 206.0
28 TraesCS3B01G377600 chr2B 81.714 175 30 2 3418 3591 680346121 680346294 1.180000e-30 145.0
29 TraesCS3B01G377600 chr2B 97.778 45 1 0 807 851 91498432 91498388 1.210000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G377600 chr3B 594742353 594746416 4063 True 7505.0 7505 100.0000 1 4064 1 chr3B.!!$R1 4063
1 TraesCS3B01G377600 chr3B 680233922 680235317 1395 True 2170.0 2170 94.7030 1248 2651 1 chr3B.!!$R2 1403
2 TraesCS3B01G377600 chr3B 733621798 733623186 1388 False 2154.0 2154 94.6060 1248 2646 1 chr3B.!!$F1 1398
3 TraesCS3B01G377600 chr3A 595059223 595062515 3292 True 2147.5 4193 93.2525 97 3375 2 chr3A.!!$R1 3278
4 TraesCS3B01G377600 chr3A 574232407 574233029 622 False 579.0 579 83.7880 3440 4049 1 chr3A.!!$F1 609
5 TraesCS3B01G377600 chr3D 452617124 452620953 3829 True 2336.5 4109 90.3130 97 3410 2 chr3D.!!$R1 3313
6 TraesCS3B01G377600 chr5B 411025392 411026787 1395 True 2165.0 2165 94.6330 1248 2651 1 chr5B.!!$R2 1403
7 TraesCS3B01G377600 chr1B 353272563 353273958 1395 True 2154.0 2154 94.4920 1248 2651 1 chr1B.!!$R1 1403
8 TraesCS3B01G377600 chr1B 532693355 532695255 1900 False 1541.0 1541 81.4390 1086 2989 1 chr1B.!!$F1 1903
9 TraesCS3B01G377600 chr7A 608482219 608483607 1388 False 2148.0 2148 94.5350 1248 2646 1 chr7A.!!$F1 1398
10 TraesCS3B01G377600 chr7A 85361252 85361905 653 True 630.0 630 84.4040 3424 4064 1 chr7A.!!$R1 640
11 TraesCS3B01G377600 chr6B 424069782 424071170 1388 False 2143.0 2143 94.4640 1248 2646 1 chr6B.!!$F1 1398
12 TraesCS3B01G377600 chr1D 397285115 397287015 1900 False 1585.0 1585 81.8470 1086 2989 1 chr1D.!!$F1 1903
13 TraesCS3B01G377600 chr4B 396523548 396524267 719 True 1062.0 1062 93.3240 1928 2651 1 chr4B.!!$R2 723
14 TraesCS3B01G377600 chrUn 363668711 363669373 662 False 1044.0 1044 94.8300 1970 2646 1 chrUn.!!$F1 676
15 TraesCS3B01G377600 chr7B 423763521 423764182 661 True 1011.0 1011 94.5620 3414 4062 1 chr7B.!!$R1 648
16 TraesCS3B01G377600 chr6D 3288734 3289325 591 True 436.0 436 80.5320 3420 4002 1 chr6D.!!$R1 582
17 TraesCS3B01G377600 chr2D 55138948 55139540 592 True 436.0 436 80.3030 3421 4001 1 chr2D.!!$R1 580
18 TraesCS3B01G377600 chr4D 253780345 253780934 589 False 416.0 416 79.8990 3422 4002 1 chr4D.!!$F1 580

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
388 411 0.028770 GAGCTCGACGACCTGATCTG 59.971 60.0 0.00 0.0 0.00 2.90 F
673 1157 0.098025 CGGGCGCAATAACAACGATT 59.902 50.0 10.83 0.0 0.00 3.34 F
976 1506 0.399806 ATCTTCCTCCTCTCCAGGCC 60.400 60.0 0.00 0.0 40.12 5.19 F
2691 3249 1.657751 CCATCAGCGACGAGGAGACA 61.658 60.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 2910 0.982852 TGTTGGCCTCGAGGATGGAT 60.983 55.000 35.69 0.00 37.39 3.41 R
2521 3079 1.727022 GCTTTTCGACGACGGACGA 60.727 57.895 13.52 13.52 45.77 4.20 R
2739 3297 1.273688 CGCCGTCGATGTTGACAATA 58.726 50.000 3.52 0.00 38.84 1.90 R
3859 4482 0.036732 TGTTGCGCTGGATCTTCCTT 59.963 50.000 9.73 0.00 37.46 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.910039 ACCCCTGGCGGTAAGAAA 58.090 55.556 5.20 0.00 33.04 2.52
18 19 2.156920 ACCCCTGGCGGTAAGAAAA 58.843 52.632 5.20 0.00 33.04 2.29
19 20 0.479378 ACCCCTGGCGGTAAGAAAAA 59.521 50.000 5.20 0.00 33.04 1.94
20 21 1.173913 CCCCTGGCGGTAAGAAAAAG 58.826 55.000 0.00 0.00 0.00 2.27
21 22 1.173913 CCCTGGCGGTAAGAAAAAGG 58.826 55.000 0.00 0.00 0.00 3.11
22 23 1.173913 CCTGGCGGTAAGAAAAAGGG 58.826 55.000 0.00 0.00 0.00 3.95
23 24 1.546998 CCTGGCGGTAAGAAAAAGGGT 60.547 52.381 0.00 0.00 0.00 4.34
24 25 1.810755 CTGGCGGTAAGAAAAAGGGTC 59.189 52.381 0.00 0.00 0.00 4.46
25 26 1.143277 TGGCGGTAAGAAAAAGGGTCA 59.857 47.619 0.00 0.00 0.00 4.02
26 27 1.810755 GGCGGTAAGAAAAAGGGTCAG 59.189 52.381 0.00 0.00 0.00 3.51
27 28 2.551504 GGCGGTAAGAAAAAGGGTCAGA 60.552 50.000 0.00 0.00 0.00 3.27
28 29 3.344515 GCGGTAAGAAAAAGGGTCAGAT 58.655 45.455 0.00 0.00 0.00 2.90
29 30 3.374367 GCGGTAAGAAAAAGGGTCAGATC 59.626 47.826 0.00 0.00 0.00 2.75
30 31 4.833390 CGGTAAGAAAAAGGGTCAGATCT 58.167 43.478 0.00 0.00 0.00 2.75
31 32 4.870991 CGGTAAGAAAAAGGGTCAGATCTC 59.129 45.833 0.00 0.00 0.00 2.75
32 33 5.568825 CGGTAAGAAAAAGGGTCAGATCTCA 60.569 44.000 0.00 0.00 0.00 3.27
33 34 6.238648 GGTAAGAAAAAGGGTCAGATCTCAA 58.761 40.000 0.00 0.00 0.00 3.02
34 35 6.715264 GGTAAGAAAAAGGGTCAGATCTCAAA 59.285 38.462 0.00 0.00 0.00 2.69
35 36 7.230712 GGTAAGAAAAAGGGTCAGATCTCAAAA 59.769 37.037 0.00 0.00 0.00 2.44
36 37 7.660030 AAGAAAAAGGGTCAGATCTCAAAAA 57.340 32.000 0.00 0.00 0.00 1.94
71 72 7.470289 CGGAATCGGATCCTGAATTTATATC 57.530 40.000 10.75 0.00 37.34 1.63
72 73 7.041721 CGGAATCGGATCCTGAATTTATATCA 58.958 38.462 10.75 0.00 37.34 2.15
73 74 7.549134 CGGAATCGGATCCTGAATTTATATCAA 59.451 37.037 10.75 0.00 37.34 2.57
74 75 9.231297 GGAATCGGATCCTGAATTTATATCAAA 57.769 33.333 10.75 0.00 36.50 2.69
77 78 9.799106 ATCGGATCCTGAATTTATATCAAAAGT 57.201 29.630 10.75 0.00 0.00 2.66
78 79 9.056005 TCGGATCCTGAATTTATATCAAAAGTG 57.944 33.333 10.75 0.00 0.00 3.16
79 80 8.840321 CGGATCCTGAATTTATATCAAAAGTGT 58.160 33.333 10.75 0.00 0.00 3.55
129 130 1.140161 CCGCCAAGTTGCCATGATG 59.860 57.895 0.00 0.00 0.00 3.07
170 185 1.761784 CTCATTCAGGAGGGAGTCAGG 59.238 57.143 0.00 0.00 0.00 3.86
198 213 0.817634 TGGACGTTTGCCTCAAGGTG 60.818 55.000 0.00 0.00 37.57 4.00
204 221 1.807142 GTTTGCCTCAAGGTGCTACTC 59.193 52.381 0.00 0.00 37.57 2.59
211 228 3.260884 CCTCAAGGTGCTACTCCTTTGTA 59.739 47.826 0.00 0.00 42.57 2.41
212 229 4.080863 CCTCAAGGTGCTACTCCTTTGTAT 60.081 45.833 0.00 0.00 42.57 2.29
231 248 5.587289 TGTATTTGTTTCAAGTGGAACAGC 58.413 37.500 5.35 0.14 41.80 4.40
233 250 3.502191 TTGTTTCAAGTGGAACAGCAC 57.498 42.857 5.35 0.00 41.80 4.40
258 275 3.214328 TCAAGGAAGGAAAACTGCACTC 58.786 45.455 0.00 0.00 0.00 3.51
296 313 2.307049 CTGCGTTGTCGAACAAAATCC 58.693 47.619 0.00 0.00 40.15 3.01
343 361 1.222300 ACAACGATGTTGCGTGCTAA 58.778 45.000 9.45 0.00 44.86 3.09
388 411 0.028770 GAGCTCGACGACCTGATCTG 59.971 60.000 0.00 0.00 0.00 2.90
389 412 0.393132 AGCTCGACGACCTGATCTGA 60.393 55.000 0.38 0.00 0.00 3.27
545 590 1.261480 AACACCTCGAGCTGACTCAT 58.739 50.000 14.61 0.00 43.66 2.90
579 624 2.692368 GGACTGATCCAGCCCCCA 60.692 66.667 0.00 0.00 45.47 4.96
580 625 2.081161 GGACTGATCCAGCCCCCAT 61.081 63.158 0.00 0.00 45.47 4.00
584 629 2.451294 GATCCAGCCCCCATCCCT 60.451 66.667 0.00 0.00 0.00 4.20
585 630 2.780040 ATCCAGCCCCCATCCCTG 60.780 66.667 0.00 0.00 0.00 4.45
593 638 2.780040 CCCATCCCTGCCCTCCAT 60.780 66.667 0.00 0.00 0.00 3.41
594 639 2.397902 CCCATCCCTGCCCTCCATT 61.398 63.158 0.00 0.00 0.00 3.16
595 640 1.152368 CCATCCCTGCCCTCCATTC 59.848 63.158 0.00 0.00 0.00 2.67
596 641 1.152368 CATCCCTGCCCTCCATTCC 59.848 63.158 0.00 0.00 0.00 3.01
597 642 1.006631 ATCCCTGCCCTCCATTCCT 59.993 57.895 0.00 0.00 0.00 3.36
598 643 0.628668 ATCCCTGCCCTCCATTCCTT 60.629 55.000 0.00 0.00 0.00 3.36
599 644 0.850883 TCCCTGCCCTCCATTCCTTT 60.851 55.000 0.00 0.00 0.00 3.11
617 662 4.552365 CCATCCGACGGCCAGCAT 62.552 66.667 9.66 0.00 0.00 3.79
629 674 4.753662 CAGCATGCCACAGCCCCT 62.754 66.667 15.66 0.00 38.69 4.79
669 1153 1.587933 TTCCCGGGCGCAATAACAAC 61.588 55.000 18.49 0.00 0.00 3.32
673 1157 0.098025 CGGGCGCAATAACAACGATT 59.902 50.000 10.83 0.00 0.00 3.34
677 1162 4.356289 GGGCGCAATAACAACGATTAAAT 58.644 39.130 10.83 0.00 0.00 1.40
687 1172 5.296813 ACAACGATTAAATCCAGAGCAAC 57.703 39.130 0.00 0.00 0.00 4.17
688 1173 4.759693 ACAACGATTAAATCCAGAGCAACA 59.240 37.500 0.00 0.00 0.00 3.33
689 1174 5.415701 ACAACGATTAAATCCAGAGCAACAT 59.584 36.000 0.00 0.00 0.00 2.71
767 1263 4.772046 AATTTCCGTGATACGACATTCG 57.228 40.909 2.52 0.00 46.05 3.34
833 1344 1.434188 TCCAGCTCTCAAAGTCCCAA 58.566 50.000 0.00 0.00 0.00 4.12
840 1351 0.951558 CTCAAAGTCCCAACCAACCG 59.048 55.000 0.00 0.00 0.00 4.44
868 1391 3.187227 CCACCAGCTTATTACATCATCGC 59.813 47.826 0.00 0.00 0.00 4.58
901 1428 2.282251 TCACTCCACTCCGTCGCT 60.282 61.111 0.00 0.00 0.00 4.93
948 1478 2.129607 CGTAATACCATTTCCGTCCGG 58.870 52.381 0.00 0.00 0.00 5.14
972 1502 1.561542 GCCAAATCTTCCTCCTCTCCA 59.438 52.381 0.00 0.00 0.00 3.86
973 1503 2.421248 GCCAAATCTTCCTCCTCTCCAG 60.421 54.545 0.00 0.00 0.00 3.86
975 1505 1.506025 AATCTTCCTCCTCTCCAGGC 58.494 55.000 0.00 0.00 40.12 4.85
976 1506 0.399806 ATCTTCCTCCTCTCCAGGCC 60.400 60.000 0.00 0.00 40.12 5.19
977 1507 2.041265 TTCCTCCTCTCCAGGCCC 59.959 66.667 0.00 0.00 40.12 5.80
978 1508 3.642741 TTCCTCCTCTCCAGGCCCC 62.643 68.421 0.00 0.00 40.12 5.80
980 1510 4.421554 CTCCTCTCCAGGCCCCCA 62.422 72.222 0.00 0.00 40.12 4.96
981 1511 3.950861 CTCCTCTCCAGGCCCCCAA 62.951 68.421 0.00 0.00 40.12 4.12
1737 2282 2.969238 GCCATGATCGCCCTCGTG 60.969 66.667 0.00 0.00 36.96 4.35
2352 2910 3.642778 GACCGCGCTGCTCAACCTA 62.643 63.158 5.56 0.00 0.00 3.08
2397 2955 4.451150 ATCATGCACGCCGACGGT 62.451 61.111 16.73 0.00 46.04 4.83
2691 3249 1.657751 CCATCAGCGACGAGGAGACA 61.658 60.000 0.00 0.00 0.00 3.41
2967 3525 4.221422 GCGTCGCTGGGCAGGATA 62.221 66.667 10.68 0.00 0.00 2.59
3161 3724 5.869344 CGAGAGATAACAAAATGGTGAGTGA 59.131 40.000 0.00 0.00 0.00 3.41
3213 3815 8.089597 CCGTTTGTATACCAAAATTTTACCCTT 58.910 33.333 2.44 0.00 44.36 3.95
3233 3838 6.017357 ACCCTTTTCTTCTTGACACGAAATAC 60.017 38.462 0.00 0.00 0.00 1.89
3239 3844 7.576750 TCTTCTTGACACGAAATACACATAC 57.423 36.000 0.00 0.00 0.00 2.39
3240 3845 7.149307 TCTTCTTGACACGAAATACACATACA 58.851 34.615 0.00 0.00 0.00 2.29
3241 3846 6.699895 TCTTGACACGAAATACACATACAC 57.300 37.500 0.00 0.00 0.00 2.90
3245 3850 7.247929 TGACACGAAATACACATACACAAAA 57.752 32.000 0.00 0.00 0.00 2.44
3246 3851 7.348956 TGACACGAAATACACATACACAAAAG 58.651 34.615 0.00 0.00 0.00 2.27
3247 3852 7.011576 TGACACGAAATACACATACACAAAAGT 59.988 33.333 0.00 0.00 0.00 2.66
3248 3853 7.699566 ACACGAAATACACATACACAAAAGTT 58.300 30.769 0.00 0.00 0.00 2.66
3261 3866 3.249917 ACAAAAGTTGTGAAAGCGGTTG 58.750 40.909 0.00 0.00 43.48 3.77
3289 3894 1.610363 TGTGTTGTGTTGTGGTGTGT 58.390 45.000 0.00 0.00 0.00 3.72
3384 3989 1.792367 GGGAAAGCAACGCATTTGTTC 59.208 47.619 0.00 0.00 37.54 3.18
3410 4020 3.203412 CGGTCTCCGTCCTCTCCG 61.203 72.222 0.00 0.00 42.73 4.63
3411 4021 2.045143 GGTCTCCGTCCTCTCCGT 60.045 66.667 0.00 0.00 0.00 4.69
3412 4022 2.408241 GGTCTCCGTCCTCTCCGTG 61.408 68.421 0.00 0.00 0.00 4.94
3418 4028 1.320344 CCGTCCTCTCCGTGATCCAA 61.320 60.000 0.00 0.00 0.00 3.53
3450 4060 2.580966 AGAGAACGTCGGCCTTTATC 57.419 50.000 0.00 0.00 0.00 1.75
3514 4124 7.931578 TCCAGAGTAGAAAGAAAAACACAAA 57.068 32.000 0.00 0.00 0.00 2.83
3701 4324 1.860950 CAGTCAGAGTGAAACACCACG 59.139 52.381 0.00 0.00 41.43 4.94
3742 4365 2.202974 CAGCCTAGCAGCGCATCA 60.203 61.111 11.47 0.00 38.01 3.07
3876 4499 0.677731 CCAAGGAAGATCCAGCGCAA 60.678 55.000 11.47 0.00 39.61 4.85
3911 4534 4.887190 ACAAAACCCTGCGGCGGT 62.887 61.111 9.78 0.37 34.07 5.68
3978 4601 0.737715 GAGAGGCTTGTACAGGTGCG 60.738 60.000 6.86 0.00 0.00 5.34
4036 4659 0.677414 GTTCGTCGAGGAGGAGGAGT 60.677 60.000 7.98 0.00 32.97 3.85
4051 4674 1.198713 GGAGTCTCAGGCTCATTCCA 58.801 55.000 8.95 0.00 34.83 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.479378 TTTTTCTTACCGCCAGGGGT 59.521 50.000 11.48 11.48 43.47 4.95
1 2 1.173913 CTTTTTCTTACCGCCAGGGG 58.826 55.000 0.00 0.00 43.47 4.79
2 3 1.173913 CCTTTTTCTTACCGCCAGGG 58.826 55.000 0.00 0.00 43.47 4.45
3 4 1.173913 CCCTTTTTCTTACCGCCAGG 58.826 55.000 0.00 0.00 45.13 4.45
4 5 1.810755 GACCCTTTTTCTTACCGCCAG 59.189 52.381 0.00 0.00 0.00 4.85
5 6 1.143277 TGACCCTTTTTCTTACCGCCA 59.857 47.619 0.00 0.00 0.00 5.69
6 7 1.810755 CTGACCCTTTTTCTTACCGCC 59.189 52.381 0.00 0.00 0.00 6.13
7 8 2.774687 TCTGACCCTTTTTCTTACCGC 58.225 47.619 0.00 0.00 0.00 5.68
8 9 4.833390 AGATCTGACCCTTTTTCTTACCG 58.167 43.478 0.00 0.00 0.00 4.02
9 10 5.805728 TGAGATCTGACCCTTTTTCTTACC 58.194 41.667 0.00 0.00 0.00 2.85
10 11 7.745620 TTTGAGATCTGACCCTTTTTCTTAC 57.254 36.000 0.00 0.00 0.00 2.34
11 12 8.760980 TTTTTGAGATCTGACCCTTTTTCTTA 57.239 30.769 0.00 0.00 0.00 2.10
12 13 7.660030 TTTTTGAGATCTGACCCTTTTTCTT 57.340 32.000 0.00 0.00 0.00 2.52
47 48 7.041721 TGATATAAATTCAGGATCCGATTCCG 58.958 38.462 5.98 0.00 40.94 4.30
48 49 8.792830 TTGATATAAATTCAGGATCCGATTCC 57.207 34.615 5.98 0.00 35.90 3.01
51 52 9.799106 ACTTTTGATATAAATTCAGGATCCGAT 57.201 29.630 5.98 0.00 0.00 4.18
52 53 9.056005 CACTTTTGATATAAATTCAGGATCCGA 57.944 33.333 5.98 4.05 0.00 4.55
53 54 8.840321 ACACTTTTGATATAAATTCAGGATCCG 58.160 33.333 5.98 1.36 0.00 4.18
67 68 9.528018 AATTTCGTGTTTTGACACTTTTGATAT 57.472 25.926 7.92 0.00 38.40 1.63
68 69 8.918961 AATTTCGTGTTTTGACACTTTTGATA 57.081 26.923 7.92 0.00 38.40 2.15
69 70 7.826260 AATTTCGTGTTTTGACACTTTTGAT 57.174 28.000 7.92 0.00 38.40 2.57
70 71 7.644986 AAATTTCGTGTTTTGACACTTTTGA 57.355 28.000 7.92 0.00 38.40 2.69
71 72 7.630606 GCTAAATTTCGTGTTTTGACACTTTTG 59.369 33.333 7.92 4.47 38.40 2.44
72 73 7.462200 CGCTAAATTTCGTGTTTTGACACTTTT 60.462 33.333 7.92 5.52 38.40 2.27
73 74 6.020995 CGCTAAATTTCGTGTTTTGACACTTT 60.021 34.615 7.92 4.59 38.40 2.66
74 75 5.454232 CGCTAAATTTCGTGTTTTGACACTT 59.546 36.000 7.92 0.00 38.40 3.16
75 76 4.967575 CGCTAAATTTCGTGTTTTGACACT 59.032 37.500 7.92 0.00 38.40 3.55
76 77 4.965158 TCGCTAAATTTCGTGTTTTGACAC 59.035 37.500 0.00 0.00 37.27 3.67
77 78 5.158101 TCGCTAAATTTCGTGTTTTGACA 57.842 34.783 0.00 0.00 0.00 3.58
78 79 4.611366 CCTCGCTAAATTTCGTGTTTTGAC 59.389 41.667 0.00 0.00 0.00 3.18
79 80 4.273969 ACCTCGCTAAATTTCGTGTTTTGA 59.726 37.500 0.00 0.00 0.00 2.69
80 81 4.533222 ACCTCGCTAAATTTCGTGTTTTG 58.467 39.130 0.00 0.00 0.00 2.44
81 82 4.609783 CGACCTCGCTAAATTTCGTGTTTT 60.610 41.667 0.00 0.00 0.00 2.43
82 83 3.120786 CGACCTCGCTAAATTTCGTGTTT 60.121 43.478 0.00 0.00 0.00 2.83
83 84 2.410730 CGACCTCGCTAAATTTCGTGTT 59.589 45.455 0.00 0.00 0.00 3.32
84 85 1.990563 CGACCTCGCTAAATTTCGTGT 59.009 47.619 0.00 0.00 0.00 4.49
85 86 2.696076 CGACCTCGCTAAATTTCGTG 57.304 50.000 0.00 0.00 0.00 4.35
170 185 2.030274 AGGCAAACGTCCAACTAATTGC 60.030 45.455 8.44 8.44 41.69 3.56
198 213 7.591426 CACTTGAAACAAATACAAAGGAGTAGC 59.409 37.037 0.00 0.00 0.00 3.58
204 221 7.038659 TGTTCCACTTGAAACAAATACAAAGG 58.961 34.615 0.00 0.00 33.94 3.11
211 228 4.432712 GTGCTGTTCCACTTGAAACAAAT 58.567 39.130 0.00 0.00 33.94 2.32
212 229 3.671971 CGTGCTGTTCCACTTGAAACAAA 60.672 43.478 0.00 0.00 33.94 2.83
231 248 1.266989 GTTTTCCTTCCTTGAGGCGTG 59.733 52.381 0.00 0.00 36.71 5.34
233 250 1.537202 CAGTTTTCCTTCCTTGAGGCG 59.463 52.381 0.00 0.00 36.71 5.52
258 275 0.035458 AGGCTTCACGAGGGAAACAG 59.965 55.000 0.00 0.00 0.00 3.16
328 346 0.247419 CTGCTTAGCACGCAACATCG 60.247 55.000 1.39 0.00 36.88 3.84
388 411 4.776795 TTTTTGCTTTTACCGGGAGATC 57.223 40.909 6.32 0.00 0.00 2.75
389 412 4.081697 CCATTTTTGCTTTTACCGGGAGAT 60.082 41.667 6.32 0.00 0.00 2.75
579 624 0.628668 AAGGAATGGAGGGCAGGGAT 60.629 55.000 0.00 0.00 0.00 3.85
580 625 0.850883 AAAGGAATGGAGGGCAGGGA 60.851 55.000 0.00 0.00 0.00 4.20
584 629 1.009997 ATGGAAAGGAATGGAGGGCA 58.990 50.000 0.00 0.00 0.00 5.36
585 630 1.697284 GATGGAAAGGAATGGAGGGC 58.303 55.000 0.00 0.00 0.00 5.19
586 631 1.477558 CGGATGGAAAGGAATGGAGGG 60.478 57.143 0.00 0.00 0.00 4.30
587 632 1.490490 TCGGATGGAAAGGAATGGAGG 59.510 52.381 0.00 0.00 0.00 4.30
588 633 2.565841 GTCGGATGGAAAGGAATGGAG 58.434 52.381 0.00 0.00 0.00 3.86
589 634 1.134521 CGTCGGATGGAAAGGAATGGA 60.135 52.381 0.00 0.00 0.00 3.41
590 635 1.299541 CGTCGGATGGAAAGGAATGG 58.700 55.000 0.00 0.00 0.00 3.16
591 636 1.299541 CCGTCGGATGGAAAGGAATG 58.700 55.000 10.90 0.00 0.00 2.67
592 637 0.463833 GCCGTCGGATGGAAAGGAAT 60.464 55.000 20.37 0.00 0.00 3.01
593 638 1.078708 GCCGTCGGATGGAAAGGAA 60.079 57.895 20.37 0.00 0.00 3.36
594 639 2.582436 GCCGTCGGATGGAAAGGA 59.418 61.111 20.37 0.00 0.00 3.36
595 640 2.513897 GGCCGTCGGATGGAAAGG 60.514 66.667 20.37 0.00 0.00 3.11
596 641 1.815421 CTGGCCGTCGGATGGAAAG 60.815 63.158 20.37 11.61 0.00 2.62
597 642 2.267642 CTGGCCGTCGGATGGAAA 59.732 61.111 20.37 5.84 0.00 3.13
598 643 4.467084 GCTGGCCGTCGGATGGAA 62.467 66.667 20.37 6.20 0.00 3.53
669 1153 5.739752 TGATGTTGCTCTGGATTTAATCG 57.260 39.130 0.00 0.00 0.00 3.34
673 1157 6.358991 TGATGATGATGTTGCTCTGGATTTA 58.641 36.000 0.00 0.00 0.00 1.40
677 1162 3.918294 TGATGATGATGTTGCTCTGGA 57.082 42.857 0.00 0.00 0.00 3.86
687 1172 2.747436 ACGACGGTGATGATGATGATG 58.253 47.619 0.00 0.00 0.00 3.07
688 1173 3.459232 AACGACGGTGATGATGATGAT 57.541 42.857 0.00 0.00 0.00 2.45
689 1174 2.959507 AACGACGGTGATGATGATGA 57.040 45.000 0.00 0.00 0.00 2.92
739 1231 7.169035 TGTCGTATCACGGAAATTATTTAGC 57.831 36.000 0.00 0.00 42.81 3.09
767 1263 8.958043 GGTGTTGATCTTATTTTATCGATTTGC 58.042 33.333 1.71 0.00 0.00 3.68
840 1351 2.618368 TAATAAGCTGGTGGGCCGCC 62.618 60.000 29.44 29.44 37.67 6.13
868 1391 8.029642 AGTGGAGTGAGATTTTTGTTATTACG 57.970 34.615 0.00 0.00 0.00 3.18
948 1478 0.253327 AGGAGGAAGATTTGGCGGAC 59.747 55.000 0.00 0.00 0.00 4.79
2148 2706 3.764434 AGAGCTTCTTCACCAGATACGAA 59.236 43.478 0.00 0.00 0.00 3.85
2352 2910 0.982852 TGTTGGCCTCGAGGATGGAT 60.983 55.000 35.69 0.00 37.39 3.41
2521 3079 1.727022 GCTTTTCGACGACGGACGA 60.727 57.895 13.52 13.52 45.77 4.20
2607 3165 2.038007 TTCTCCCTCTCGCCTGCT 59.962 61.111 0.00 0.00 0.00 4.24
2739 3297 1.273688 CGCCGTCGATGTTGACAATA 58.726 50.000 3.52 0.00 38.84 1.90
2742 3300 3.109547 GCGCCGTCGATGTTGACA 61.110 61.111 3.52 0.00 38.84 3.58
3077 3635 3.879998 TGTGGTTTGTACAAGAAGAGCA 58.120 40.909 8.56 7.07 0.00 4.26
3213 3815 6.912203 TGTGTATTTCGTGTCAAGAAGAAA 57.088 33.333 1.46 0.12 37.07 2.52
3240 3845 3.249917 CAACCGCTTTCACAACTTTTGT 58.750 40.909 0.00 0.00 46.75 2.83
3241 3846 2.602660 CCAACCGCTTTCACAACTTTTG 59.397 45.455 0.00 0.00 0.00 2.44
3245 3850 1.733526 GCCAACCGCTTTCACAACT 59.266 52.632 0.00 0.00 0.00 3.16
3246 3851 4.319249 GCCAACCGCTTTCACAAC 57.681 55.556 0.00 0.00 0.00 3.32
3255 3860 3.276846 ACAACACGAGCCAACCGC 61.277 61.111 0.00 0.00 37.98 5.68
3261 3866 0.450184 AACACAACACAACACGAGCC 59.550 50.000 0.00 0.00 0.00 4.70
3266 3871 2.287909 ACACCACAACACAACACAACAC 60.288 45.455 0.00 0.00 0.00 3.32
3267 3872 1.957177 ACACCACAACACAACACAACA 59.043 42.857 0.00 0.00 0.00 3.33
3268 3873 2.287909 ACACACCACAACACAACACAAC 60.288 45.455 0.00 0.00 0.00 3.32
3269 3874 1.957177 ACACACCACAACACAACACAA 59.043 42.857 0.00 0.00 0.00 3.33
3270 3875 1.268079 CACACACCACAACACAACACA 59.732 47.619 0.00 0.00 0.00 3.72
3306 3911 0.397535 TAAGGCGGACCGGTTATCCT 60.398 55.000 17.22 12.67 42.76 3.24
3395 4005 0.748729 ATCACGGAGAGGACGGAGAC 60.749 60.000 0.00 0.00 35.23 3.36
3399 4009 1.320344 TTGGATCACGGAGAGGACGG 61.320 60.000 0.00 0.00 35.23 4.79
3430 4040 2.232941 TGATAAAGGCCGACGTTCTCTT 59.767 45.455 0.00 0.00 0.00 2.85
3450 4060 8.825745 ACTTTGTGTAATTTGGTTGCTTAATTG 58.174 29.630 0.00 0.00 0.00 2.32
3493 4103 8.794335 AGTCTTTGTGTTTTTCTTTCTACTCT 57.206 30.769 0.00 0.00 0.00 3.24
3514 4124 5.830991 AGTCTAGTTTGAACTCTGTGAGTCT 59.169 40.000 0.00 0.00 42.59 3.24
3599 4222 2.037121 TGTTGCTGAGATCAAGACGGAA 59.963 45.455 0.00 0.00 0.00 4.30
3701 4324 2.347731 CGGGAGAAGCACTTTCCTAAC 58.652 52.381 9.79 0.00 36.40 2.34
3859 4482 0.036732 TGTTGCGCTGGATCTTCCTT 59.963 50.000 9.73 0.00 37.46 3.36
3876 4499 1.417517 TGTGCAAGTGTCCTCTGATGT 59.582 47.619 0.00 0.00 0.00 3.06
3911 4534 1.985159 TCTAGCTTTTCTTGGGCTCCA 59.015 47.619 0.00 0.00 37.50 3.86
3978 4601 3.679389 CCTATGTTGATATGGTGCTCCC 58.321 50.000 1.59 0.00 0.00 4.30
4036 4659 1.219124 GCGTGGAATGAGCCTGAGA 59.781 57.895 0.00 0.00 0.00 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.